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Portuguese Platform of BioImaging (PPBI)
Hosting Legal Entity
Self-standing RI
Legal Status
Rua Alfredo Allen 208, i3S building, Porto, PO: 4200 (Portugal)
Type Of RI
Coordinating Country
Participating Countries
Provider Country:
CBMR - Centre for Biomedical Research (@ University of Algarve) | CEDOC - Chronic Diseases Research Center (@ NOVA) | Champalimaud Foundation | CICS-UBI fluorescence microscopy facility | CNC-UC - Centro de Neurociências e Biologia Celular da Universidade de Coimbra (CNC-UC) | Faculdade de Ciências da Universidade de Lisboa | IBMC - Institute for Molecular and Cell Biology | ICVS - Life and Health Sciences Research Institute (@Universidade do Minho) | IGC - Instituto Gulbenkian de Ciência | IMM - Instituto de Medicina Molecular João Lobo Antunes | INEB - Instituto Nacional de Engenharia Biomédica | Instituto Superior Técnico da Universidade de Lisboa | ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier | Universidade de Aveiro | Universidade de Coimbra
Current Status:
Operational since 2018
Scientific Description
The PPBI is a specialized research infrastructure in Bioimaging and formed by a national consortium of Portuguese Research Institutes and Universities of excellence. The activity of PPBI is focused on providing shared access to advanced Bioimaging resources and support research in life sciences attain greater expertise in the areas of cell and developmental biology, neurosciences, oncobiology, immunology, infection and regenerative medicine.Our aims: a) Create an infrastructure to rationalize and maximize technical capabilities and resources in Advanced Microscopy and Bioimaging in the domains of Biology, Biomedicine and Bioengineering at a national levelb) Support and foster an active collaboration between institutions, as well as provide services and competencies to the R&D community in Universities, Research institutes, companies and other private institutions, both national and international.c) Constitute a synopsis of resources, equipment, algorithms and software for image processing/analysis, methodologies, knowledge, technological development and training in Advanced Microscopy and Bioimage, placed art the service of the national and international scientific and business community.d) Promote scientific and technological development, and innovation in Advanced Microscopy and Bioimaging, providing users with unique resources and competence, in an integrated manner.e) Contribute to advanced training of human resources and their qualification in technological areas fundamental for R&D, supporting and promoting initiatives of formation and making available resources in articulation with com all institutional cosigners f) Serve the national and international R&D community, assuming itself as an infrastructure of reference, internationally competitive.

RI Keywords
Advanced microscopy, Biological Imaging (BI), Light microscopy, Confocal microscopy
RI Category
Biomedical Imaging Facilities
Scientific Domain
Biological and Medical Sciences
ESFRI Domain
Health and Food
Image Processing and Analysis

After acquiring a microscopic image, the resulting digital image is generally processed. The final outcome of the processing procedure can be either an improve image, or a set of parameters obtained from careful analysis and treatment of the image. The PPBI consortium has several image analysis & processing software either licensed or freeware that will help the analysis of the obtained data, as well as greatly enhance the final image. Among the licensed software available there are Huygens (image restoration, visualization, and analysis); Imaris (data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets); MatLab (analyze data, develop algorithms, create models and applications); IN Cell Investigator (flexible and comprehensive solution for automated high-content analysis of live and fixed assays). Among the freeware software there is Image J (display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images), Fiji (an image processing package. It can be described as a "batteries-included" distribution of ImageJ); Cell Profiler (open-source platform for automated image analysis) Cell Profiler Analyst (open-source software for exploring and analyzing large, high-dimensional image-derived data), GNU Octave (high-level language, primarily intended for numerical computation)

Development Services, Consulting, Training
Light Microscopy

PPBI comprises multiple light microscopy resources including high-end widefield microscopes, laser scanning and spinning disk confocal systems, two-photon microscopes and super-resolution. TECHNIQUES AVAILABLE: Multichannel (widefield) fluorescence imaging + transmission imaging • 3D imaging and reconstruction with laser scanning or spining disk confocals, but may also have multiphoton (2P) or light-sheet (LSM) • Multidimensional in vivo timelapse experiments (ie, equipped with incubators and environmental control) • Mosaic imaging (imaging of large areas with multiple fields and stitching of adjacent fields; eg large tissue sections or whole embryos/organs) • High throughput microscopy; typically fully automated scope with protocols for acquiring automatically multiple fields in multi-well plates or dishes • Fluorescence Recovery After Photobleaching (FRAP), Photoactivation (PA) and Photoconversion (PC) • Fluorescence Resonance Energy Transfer (FRET) • Fluorescence-Lifetime Imaging Microscopy (FLIM) and Fluorescence Correlation Spectroscopy (FCS) • High-speed live cell microscopy and analysis (typicaly acquisition of multiple images /second) • "Super Resolution" and Single Mol. Localization techniques


Mesoscopy is the whole imaging (3D) or large samples ranging from 1mm to a few cm, with techniques such as light-sheet microscopy (aka SPIM) or optical (projection) tomography (aka OPT), among others. SPIM is well suited for live imaging of small embryos such as zebrafish or drosophila, less than 2mm and ~500um thick. For larger samples it is advisable to use OPT, however, in this case imaging is limited to fixed samples. It is also possible to image fluorescence and bioluminescence in vivo using animal imagers, and have those images registered with X-ray images of the whole animal. Mesoscopy resources are available at INEB and IGC nodes.

High Content Screening

High-throughput microscopy and "high content screening" allow the automated acquisition and analysis of large numbers of cells, which may also include automatic detection and live-tracking of specific cell phenotypes/behaviours. HTM systems are available currently at IBMC, FCUL and IGC nodes, but lab support for HCS analysis expertise exists mostly at the IBMC and FCUL nodes.

Electron Microscopy

Though PPBI entails mostly facilities which specialize in optical imaging, some nodes do provide access to electron microscopy resources especially (but not limited to) projects which involve some form of correlative optical and electron microscopy (techniques generally known as CLEM - Correlative Light and Electron Microscopy, or 3D reconstruction of biological samples at EM resolution using "3D electron tomography". This possibility exists at nodes at IBMC, FCUL and IGC.

Date of last update: 07/06/2019
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